Structural dynamics of the ribosome

Abstract

Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynamics has begun to emerge from a combination of approaches, most notably cryo-EM, X-ray crystallography, and FRET. Ribosome movement occurs both on a grand scale, as in the intersubunit rotational movements that are coupled to tRNA-mRNA translocation, and in intricate localized rearrangements such as those that accompany codon-anticodon recognition and peptide bond formation. In spite of much progress, our understanding of the mechanics of translation is now beset with countless new questions, reflecting the vast molecular architecture of the ribosome itself.

Figure 1

Positions and translocation of tRNA in the 70S ribosome. (a) tRNAs bound to the A (yellow), P (orange) and E (red) sites of the T. thermophilus 70S ribosome [60]. mRNA (green) and Shine-Dalgarno helix are indicated. Molecular features are indicated by color: 16S rRNA (cyan), small subunit proteins (blue), 23S rRNA (grey), 5S rRNA (light blue) and large subunit proteins (magenta). The model was constructed by superimposing the A-site tRNA and the SD helix from their corresponding 70S complexes [35,47] into the 2.8 Å structure of the T. thermophilus 70S ribosome [31]. (b) Translocation of tRNA from the A and P sites to the P and E sites, respectively. (c) 30S solvent view and (d) A-site view of cryo-EM maps for the non-ratcheted (70S•tRNA, left) and ratcheted (70S•tRNA•EF-G•GDPNP, right) states of the 70S ribosome. In panels c and d the 30S and 50S subunits are shown in yellow and light blue and the tRNA and EF-G in green and red, respectively. The figures in panels c and d were adapted from references [12,61].

Figure 2

Large-scale intrasubunit movements. (a) Movement of the 30S subunit head. Trajectories of phosphorus (blue) and Cα (dark blue) atoms demonstrating movement of the head between two crystallographically determined positions for tRNA-containing T. thermophilus ribosomes [35] and vacant E. coli [27] ribosomes. The figure is adapted from reference [27]. (b) Movement of the L1 stalk of the 50S subunit. Interaction of the elbow of E-site tRNA [60] with 23S rRNA in the L1 stalk [34] causes a large-scale displacement of the stalk (blue) relative to its position in the vacant ribosome (magenta; grey shows modeled portion of L1 stalk rRNA). (c) Movement of the L1 and L11 stalks between conformations I (magenta) and II (grey) of vacant E. coli ribosomes [27]. (d) Detailed view of (c) showing movement of the L11 stalk [27].

Figure 3

Rearrangements of nucleotides in the decoding center of the 30S subunit. (a) Vacant A site of the 30S subunit [62] (PDB 1J5E). (b) IF1 (pink) bound to the 30S subunit [56] (PDB 1HR0). (c) Cognate tRNA (yellow) bound to its mRNA codon (green) in the A site of the 70S ribosome in the presence of paromomycin [31] (PDB 2J00, 2J01). (d) Release factor RF1 (yellow) bound to a UAA stop codon (green) in a 70S termination complex [30]. 16S rRNA nucleotides G530, A1492 and A1493 are shown in cyan and 23S rRNA nucleotide A1913 is shown in grey.

Figure 4

Changes in the conformation of the binding pocket for the peptidyl moiety of the P-site tRNA in the peptidyl transferase center. (a) 70S ribosome with vacant P and A sites [27] (PDB 2AW4). (b) 50S subunit with CCA trinucleotide analogs of P-site (orange) and A-site (yellow) tRNAs [59] (PDB 1QVG). (c) 50S subunit with peptidyl-CCdApcb (orange) mimicking peptidyl-tRNA bound to the P site in the presence of sparsomycin (green) [27] (PDB 1VQ8). (d) 70S ribosome with deacylated tRNA bound to the P site (orange) (The 50S region of A-site tRNA was disordered) [31] (PDB 2J00 and 2J01). (e) and (f) Two views of a model in which the peptidyl-tRNA analog CCdApcb in (c) was superimposed on the 70S structure shown in (d). The model suggests a possible interaction of U2506 with the peptidyl moiety of the P-site tRNA (orange). The O4 and N3 positions of U2506 and the backbone amide and carbonyl groups of the aminoacyl moiety could move to within hydrogen bonding distance of each other upon minor repositioning of U2506 and the aminoacyl moiety. 23S rRNA is shown in grey.